6GR2 | pdb_00006gr2

Structure of human galactokinase in complex with galactose and ADP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d6gr2c1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6gr2c2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Galactokinase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6gr2e1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6gr2e2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Galactokinase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6gr2h1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6gr2h2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Galactokinase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6gr2g1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6gr2g2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Galactokinase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6gr2f1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6gr2f2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Galactokinase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6gr2d1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6gr2d2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Galactokinase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6gr2b1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6gr2b2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Galactokinase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6gr2a1	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	GHMP Kinase, N-terminal domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6gr2a2	Alpha and beta proteins (a+b)	Ferredoxin-like	GHMP Kinase, C-terminal domain	Galactokinase	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043715	3000100	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8043717	3001245	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8043717	3001245	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043715	3000100	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043715	3000100	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8043717	3001245	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8043717	3001245	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043715	3000100	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8043717	3001245	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043715	3000100	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043715	3000100	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8043717	3001245	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043715	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8043717	3001245	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GHMP Kinase, C-terminal domain	8043717	3001245	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043715	3000100	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	TetR_N	e6gr2C1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: TetR_N	ECOD (develop294)
E	TetR_N	e6gr2E1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: TetR_N	ECOD (develop294)
H	TetR_N	e6gr2H1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: TetR_N	ECOD (develop294)
G	TetR_N	e6gr2G1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: TetR_N	ECOD (develop294)
F	TetR_N	e6gr2F1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: TetR_N	ECOD (develop294)
D	TetR_N	e6gr2D1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: TetR_N	ECOD (develop294)
B	TetR_N	e6gr2B1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: TetR_N	ECOD (develop294)
A	V-set	e6gr2A1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: HTH	T: Ribbon-helix-helix	F: V-set	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
C	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (utative)
E	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
E	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (utative)
H	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
H	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (utative)
G	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
G	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (utative)
F	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
F	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (utative)
D	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
D	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (utative)
B	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
B	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (utative)
A	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)
A	3.30.70.890	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	GHMP kinase, C-terminal domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF08544	GHMP kinases C terminal (GHMP_kinases_C)	GHMP kinases C terminal	This family includes homoserine kinases, galactokinases and mevalonate kinases.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF10509	Galactokinase galactose-binding signature (GalKase_gal_bdg)	Galactokinase galactose-binding signature	This is the highly conserved galactokinase signature sequence which appears to be present in all galactokinases irrespective of how many other ATP binding sites, etc that they carry [1]. The function of this domain appears to be to bind galactose [2] ...	This is the highly conserved galactokinase signature sequence which appears to be present in all galactokinases irrespective of how many other ATP binding sites, etc that they carry [1]. The function of this domain appears to be to bind galactose [2], and the domain is normally at the N-terminus of the enzymes, EC:2.7.1.6 [3]. This domain is associated with the families GHMP_kinases_C, Pfam:PF08544 and GHMP_kinases_N, Pfam:PF00288.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF00288	GHMP kinases N terminal domain (GHMP_kinases_N)	GHMP kinases N terminal domain	This entry represents a conserved domain with a Gly/Ser-rich region found in galacto-, homoserine, mevalonate and phosphomevalonate kinases (GHMP) which is involved in the binding of ATP [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Galactokinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding galactose binding monosaccharide binding carbohydrate binding galactokinase activity carbohydrate kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	carbohydrate metabolic process hexitol metabolic process polyol metabolic process galactitol metabolic process primary metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process monosaccharide metabolic process carbohydrate derivative catabolic process catabolic process hexose catabolic process carbohydrate catabolic process carbohydrate metabolic process hexitol metabolic process polyol metabolic process galactitol metabolic process primary metabolic process metabolic process cellular process alcohol metabolic process small molecule metabolic process monosaccharide metabolic process carbohydrate derivative catabolic process catabolic process hexose catabolic process carbohydrate catabolic process galactose catabolic process carbohydrate derivative metabolic process organophosphate catabolic process hexose metabolic process galactose metabolic process galactose catabolic process via UDP-galactose, Leloir pathway organophosphate metabolic process phosphate-containing compound metabolic process monosaccharide catabolic process small molecule catabolic process phosphorus metabolic process glycolytic process through glucose-1-phosphate ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process pyridine-containing compound metabolic process purine ribonucleotide catabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process energy derivation by oxidation of organic compounds glycolytic process through glucose-6-phosphate purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process glycolytic process from galactose ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process glycolytic process through fructose-6-phosphate	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013750	GHMP kinase, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006206	Mevalonate/galactokinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019539	Galactokinase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036554	GHMP kinase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006204	GHMP kinase N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019741	Galactokinase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006203	GHMP kinase, ATP-binding, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000705	Galactokinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: P51570	galactosemia galactokinase deficiency cataract Lens Opacities pilocytic astrocytoma inborn errors of metabolism malignant ependymoma intellectual disability malignant glioma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.